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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:48, 17 September 2013


Full id: C1609_CD4_CD34_Mast_CD14_CD19_CD133_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:116864496..116864504,+p@chr11:116864496..116864504
+
Hg19::chr2:238512335..238512368,-p@chr2:238512335..238512368
-
Hg19::chr2:238512370..238512394,-p@chr2:238512370..238512394
-
Hg19::chr2:238512518..238512533,+p@chr2:238512518..238512533
+
Hg19::chr5:43042577..43042600,+p2@LOC153684


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
classical monocyte5.43e-5042
CD14-positive, CD16-negative classical monocyte5.43e-5042
leukocyte1.00e-43136
nongranular leukocyte1.07e-42115
defensive cell2.74e-4248
phagocyte2.74e-4248
hematopoietic lineage restricted progenitor cell6.91e-41120
myeloid leukocyte9.96e-3672
hematopoietic stem cell1.72e-34168
angioblastic mesenchymal cell1.72e-34168
myeloid lineage restricted progenitor cell1.77e-3366
granulocyte monocyte progenitor cell8.30e-3367
hematopoietic cell9.03e-32177
monopoietic cell1.49e-3159
monocyte1.49e-3159
monoblast1.49e-3159
promonocyte1.49e-3159
hematopoietic oligopotent progenitor cell2.81e-31161
hematopoietic multipotent progenitor cell2.81e-31161
macrophage dendritic cell progenitor3.58e-3061
myeloid cell7.25e-21108
common myeloid progenitor7.25e-21108
stuff accumulating cell2.16e-1887
mature alpha-beta T cell7.65e-1618
alpha-beta T cell7.65e-1618
immature T cell7.65e-1618
mature T cell7.65e-1618
immature alpha-beta T cell7.65e-1618
CD4-positive, alpha-beta T cell8.99e-136
intermediate monocyte1.14e-119
CD14-positive, CD16-positive monocyte1.14e-119
T cell1.93e-1025
pro-T cell1.93e-1025
lymphoid lineage restricted progenitor cell5.37e-1052
lymphocyte1.05e-0953
common lymphoid progenitor1.05e-0953
nucleate cell3.67e-0955
CD8-positive, alpha-beta T cell2.18e-0711
naive T cell3.26e-073
mesenchymal cell3.29e-07354
basophil6.82e-073
natural killer cell8.47e-073
pro-NK cell8.47e-073
connective tissue cell8.87e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.38e-3098
blood island3.38e-3098
bone marrow2.29e-2976
immune system3.85e-2993
hemolymphoid system2.12e-27108
bone element2.35e-2682
skeletal element5.64e-2390
skeletal system1.58e-19100
lateral plate mesoderm1.23e-08203
musculoskeletal system4.75e-08167


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.11.65981
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.11.95181
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.11.67417
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.11.89806
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ELF1#199743.406478367046030.01235066105299550.0447226506384368
FOS#235335.398773185336640.01153895317278740.0421841476621656
GATA2#262437.64695904013240.004279061879252130.0203275389405146
JUN#372537.50769751540180.004511206552906030.0213323327528277
MAX#414945.16204440720570.002526309009485180.0139956071844697



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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